In essence, CouchApp requires you to use AJAX for the entire application. Generally speaking, this bad user experience when you load skeletal markup, run JS, usually click on the server again, and then dynamically add additional markup. (unlike just loading the finished markup up). In addition, data caching is a different beast in the browser than on the server. In addition, SEO is much more complicated if you only have AJAX content.
Basically, all the reasons why you see people going against AJAX-only web applications (i.e., intrusive JavaScript) will linger in this context.
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